A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/home/rouslane/Documents/Bioinformatics-Projects/RNA-seq/02_AnalysisStepTwo/logs
General Statistics
| Sample Name | Reads | Reads mapped | % Reads mapped | % Aligned |
|---|---|---|---|---|
| SRR4420293_flagstat | 51.4M | 50.2M | 97.6% | |
| SRR4420293_hisat2 | 96.3% | |||
| SRR4420294_flagstat | 135.3M | 133.2M | 98.4% | |
| SRR4420294_hisat2 | 97.2% | |||
| SRR4420295_flagstat | 49.6M | 48.3M | 97.5% | |
| SRR4420295_hisat2 | 96.0% | |||
| SRR4420296_flagstat | 47.5M | 44.5M | 93.7% | |
| SRR4420296_hisat2 | 92.7% | |||
| SRR4420297_flagstat | 68.6M | 66.9M | 97.6% | |
| SRR4420297_hisat2 | 96.1% | |||
| SRR4420298_flagstat | 74.5M | 73.0M | 98.0% | |
| SRR4420298_hisat2 | 96.7% |
Samtools
Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352
Flagstat
This module parses the output from samtools flagstat
Flagstat: Percentage of total
This module parses the output from samtools flagstat
Bowtie 2 / HiSAT2
Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.